In that case I will file that into my box of complaints where the game never explains anything. :(
I don't really get it either. I'm guessing on your screen at the top 2/3rd of the HP bar is the "shield" you see on other players. When you take heavy damage the last third turns red, I think this is the bottom HP bar you see on players. So two thirds for shields, one third of actual HP. Though I don't think it even matters since it all acts as HP. Why they show two HP bars on enemy players? I have no idea.
I could be wrong but I believe the reasoning is that you don't get bonus damage for headshots until you remove the shield part with the exception of snipers which do enough damage to break the shield and then still headshot after.